The fastest way to learn about MARKER is to go ahead and try it out. Print out this page and follow these instructions.

Finding a gene region

Go to the home page :: http://www.gmap.net/marker

Click on 'View HapMap and other data'

In the box marked 'LocusLink gene symbol' type 'SGK2' (without the apostrophes) and click 'Go'

The next page displays datasets for the genomic region around SGK2. Depending on the marker density of these datasets, they may or may not contain markers in SGK2 itself. Go to dataset 1008522 by clicking on the blue link to that number.

Making a map

You should be at a page that shows information about dataset 1008522. Find the link that says 'Draw map' and click on that.

The next page may take a few moments to display depending on your internet connection (with a fast connection it should be less than 10 seconds). It shows a coloured graph of the |D'| statistic for this dataset. The grey boxes on the vertical axis display markers and thus indicate chromosomal position. To find out the |D'| value for any pair of markers, trace the diagonal from each marker and find the point where the two diagonals meet (just like getting the distance between two towns on a road mileage chart).

At the top of the page you'll see this statement: 'Compressed view: 1 in 3 markers are labelled'. This means that, although all the data points are plotted on the graph, to save space only 1 in 3 of the markers are labelled on the vertical axis. To see all of the markers you need to expand the map. You can do this by pressing the 'Adjust map settings' link, but don't try this yet. An alterative way is to zoom in on a specific part of the map, as described next.

Interactive features

Go down the vertical axis till you find SGK2 next to marker rs6065627 and click on either of those symbols.

The next page displays various information about marker rs6065627. Find the line that says 'Zoom in to show 20 markers around this one' and click on that button.

The next page may take a few moments to display depending on your internet connection (with a fast connection it should be less than 5 seconds). It shows a graph of the |D'| statistic for part of the dataset. This graph is more detailed and all the markers are labelled.

Click on any of the markers to get information or to recentre the zoomed map. Alternatively, try the links in the right-hand navigation panel to explore some of the different functions available for the dataset.

That's the end of the quick tour. To understand the full functionality of MARKER, go through it again and try out the different options offered at each stage. There are also demonstrations available from the home page in the news items list.